Can genomics deliver climate-change ready crops?

Abstract

Development of climate resilient crops with accelerating genetic gains in crops will require integration of different disciplines/technologies, to see the impact in the farmer's field. In this review, we summarize how we are utilizing our germplasm collections to identify superior alleles/haplotypes through NGS based sequencing approaches and how genomics-enabled technologies together with precise phenotyping are being used in crop breeding. Pre-breeding and genomics-assisted breeding approaches are contributing to the more efficient development of climate-resilient crops. It is anticipated that the integration of several disciplines/technologies will result in the delivery of climate change ready crops in less time.

Figure 1

Integrated approach for development of climate-resilient crops. This figure presents an overview on use of germplasm/genetic resources together with genomics and phenomics approaches for identification of superior alleles/haplotypes and source donors for climate-change breeding related traits. Identified lines together with genomic information can be used in pre-breeding and genomics-assisted breeding (GAB) for faster delivery of climate-resilient crops. Although sequencing/genotyping of the entire genebank for a crop will be ideal, smaller subsets of germplasm such as reference set (Ref Set), core and mini core collections can be targeted initially. Similarly, specialized genetic resources/genetic stocks such as multi-parental (nested association mapping, NAM and multi-parent advanced generation intercross, MAGIC), bi-parental (recombinant inbred lines, RILs; introgression lines, ILs; F₂) populations segregating for climate-change breeding related traits can be used. Training population (TP) can also be developed based on the specialized set of breeding lines for deployment of genomic selection (GS). These germplasm/genetic resources can be used for whole genome resequencing (WGRS) or high-density genotyping (e.g. genotyping-by-sequencing GBS, SNP-array based genotyping). High-throughput phenotyping of germplasm/genetic resources especially for climate-change breeding related traits can be undertaken using the visible light (VIS), the near-infrared (NIR) spectrum and fluorescence imaging (FLUO) in different environments (Env) by utilizing recent advances in sensors and imaging based phenotyping technologies. Analysis of these sequencing/genotyping data and phenotyping data using analytical and decision support tools (ADSTs) can provide quantitative trait loci (QTLs), marker trait associations (MTAs), quantitative trait nucleotides (QTNs), and genomic estimated breeding value (GEBVs). In addition, a catalogue of superior haplotypes and source donors for a given trait can also be identified. This information can be used in pre-breeding and GAB approaches. For instance, pre-breeding approaches by using novel donors can introduce novel alleles in the elite/cultivated genepool from the un-adapted germplasm (landraces, crop wild relatives) coming from harsh and extreme environmental conditions (simulating climate-change scenario). As a result, in addition to developing better pre-breeding lines, genetic diversity of the elite genepool can also be broadened. In the end, a number of GAB approaches such as marker assisted selection (MAS), marker-assisted recurrent selection (MARS) and GS can be deployed for integrating/accumulating superior alleles for climate-change breeding related traits. QTNs can be edited through genome editing approach called promotion of alleles through genome editing (PAGE). It is important to use ADSTs to analyze and make decision in every component of mining and integration of superior alleles in crop improvement programs. Integration of such approaches should accelerate development of climate-resilient cultivars with improved yield, enhanced resistance/tolerance to anticipated biotic and abiotic stresses and deliver higher genetics gains in farmer's fields especially in developing world.